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Coreference annotation and resolution in the Colorado Richly Annotated Full Text (CRAFT) corpus of biomedical journal articles.

Cohen KB, Lanfranchi A, Choi MJ, Bada M, Baumgartner WA Jr, Panteleyeva N, Verspoor K, Palmer M, Hunter LE.

BMC Bioinformatics. 2017 Aug 17;18(1):372. doi: 10.1186/s12859-017-1775-9.


Systems biology of facial development: contributions of ectoderm and mesenchyme.

Hooper JE, Feng W, Li H, Leach SM, Phang T, Siska C, Jones KL, Spritz RA, Hunter LE, Williams T.

Dev Biol. 2017 Jun 1;426(1):97-114. doi: 10.1016/j.ydbio.2017.03.025. Epub 2017 Mar 29.


Aging promotes acquisition of naive-like CD8+ memory T cell traits and enhanced functionalities.

Eberlein J, Davenport B, Nguyen T, Victorino F, Haist K, Jhun K, Karimpour-Fard A, Hunter L, Kedl R, Clambey ET, Homann D.

J Clin Invest. 2016 Oct 3;126(10):3942-3960. doi: 10.1172/JCI88546. Epub 2016 Sep 12.


Gene Ontology synonym generation rules lead to increased performance in biomedical concept recognition.

Funk CS, Cohen KB, Hunter LE, Verspoor KM.

J Biomed Semantics. 2016 Sep 9;7:52. doi: 10.1186/s13326-016-0096-7.


A survey of computational tools for downstream analysis of proteomic and other omic datasets.

Karimpour-Fard A, Epperson LE, Hunter LE.

Hum Genomics. 2015 Oct 28;9:28. doi: 10.1186/s40246-015-0050-2. Review.


Visual analysis of biological data-knowledge networks.

Vehlow C, Kao DP, Bristow MR, Hunter LE, Weiskopf D, Görg C.

BMC Bioinformatics. 2015 Apr 29;16:135. doi: 10.1186/s12859-015-0550-z.


KaBOB: ontology-based semantic integration of biomedical databases.

Livingston KM, Bada M, Baumgartner WA Jr, Hunter LE.

BMC Bioinformatics. 2015 Apr 23;16:126. doi: 10.1186/s12859-015-0559-3.


Rapid changes in gene expression direct rapid shifts in intestinal form and function in the Burmese python after feeding.

Andrew AL, Card DC, Ruggiero RP, Schield DR, Adams RH, Pollock DD, Secor SM, Castoe TA.

Physiol Genomics. 2015 May;47(5):147-57. doi: 10.1152/physiolgenomics.00131.2014. Epub 2015 Feb 10.


Peax: interactive visual analysis and exploration of complex clinical phenotype and gene expression association.

Hinterberg MA, Kao DP, Bristow MR, Hunter LE, Port JD, Görg C.

Pac Symp Biocomput. 2015:419-30.


Combining heterogenous data for prediction of disease related and pharmacogenes.

Funk CS, Hunter LE, Cohen KB.

Pac Symp Biocomput. 2014:328-39.


BioC: a minimalist approach to interoperability for biomedical text processing.

Comeau DC, Islamaj Doğan R, Ciccarese P, Cohen KB, Krallinger M, Leitner F, Lu Z, Peng Y, Rinaldi F, Torii M, Valencia A, Verspoor K, Wiegers TC, Wu CH, Wilbur WJ.

Database (Oxford). 2013 Sep 18;2013:bat064. doi: 10.1093/database/bat064. Print 2013.


Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology.

Hill DP, Adams N, Bada M, Batchelor C, Berardini TZ, Dietze H, Drabkin HJ, Ennis M, Foulger RE, Harris MA, Hastings J, Kale NS, de Matos P, Mungall CJ, Owen G, Roncaglia P, Steinbeck C, Turner S, Lomax J.

BMC Genomics. 2013 Jul 29;14:513. doi: 10.1186/1471-2164-14-513.


Chapter 16: text mining for translational bioinformatics.

Cohen KB, Hunter LE.

PLoS Comput Biol. 2013 Apr;9(4):e1003044. doi: 10.1371/journal.pcbi.1003044. Epub 2013 Apr 25.


Approximate subgraph matching-based literature mining for biomedical events and relations.

Liu H, Hunter L, Kešelj V, Verspoor K.

PLoS One. 2013 Apr 17;8(4):e60954. doi: 10.1371/journal.pone.0060954. Print 2013.


A corpus of full-text journal articles is a robust evaluation tool for revealing differences in performance of biomedical natural language processing tools.

Verspoor K, Cohen KB, Lanfranchi A, Warner C, Johnson HL, Roeder C, Choi JD, Funk C, Malenkiy Y, Eckert M, Xue N, Baumgartner WA Jr, Bada M, Palmer M, Hunter LE.

BMC Bioinformatics. 2012 Aug 17;13:207. doi: 10.1186/1471-2105-13-207.


Mining the pharmacogenomics literature--a survey of the state of the art.

Hahn U, Cohen KB, Garten Y, Shah NH.

Brief Bioinform. 2012 Jul;13(4):460-94. doi: 10.1093/bib/bbs018.


Concept annotation in the CRAFT corpus.

Bada M, Eckert M, Evans D, Garcia K, Shipley K, Sitnikov D, Baumgartner WA Jr, Cohen KB, Verspoor K, Blake JA, Hunter LE.

BMC Bioinformatics. 2012 Jul 9;13:161. doi: 10.1186/1471-2105-13-161.


Kidney proteome changes provide evidence for a dynamic metabolism and regional redistribution of plasma proteins during torpor-arousal cycles of hibernation.

Jani A, Orlicky DJ, Karimpour-Fard A, Epperson LE, Russell RL, Hunter LE, Martin SL.

Physiol Genomics. 2012 Jul 15;44(14):717-27. doi: 10.1152/physiolgenomics.00010.2012. Epub 2012 May 29.


Regional differences in subcutaneous adipose tissue gene expression.

Rehrer CW, Karimpour-Fard A, Hernandez TL, Law CK, Stob NR, Hunter LE, Eckel RH.

Obesity (Silver Spring). 2012 Nov;20(11):2168-73. doi: 10.1038/oby.2012.117. Epub 2012 May 4.


Synergizing genomic analysis with biological knowledge to identify and validate novel genes in pancreatic development.

Sarkar SA, Lee CE, Tipney H, Karimpour-Fard A, Dinella JD, Juhl K, Walters JA, Hutton JC, Hunter LE.

Pancreas. 2012 Aug;41(6):962-9. doi: 10.1097/MPA.0b013e31823d0160.

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